Magnesium in PDB 3iki: 5-Sme-Du Containing Dna Octamer

The structure of 5-Sme-Du Containing Dna Octamer, PDB code: 3iki was solved by J.Sheng, A.E.A.Hassan, W.Zhang, J.Gan, Z.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.32 / 1.38
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	42.882, 42.882, 23.687, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 19.4

The binding sites of Magnesium atom in the 5-Sme-Du Containing Dna Octamer (pdb code 3iki). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the 5-Sme-Du Containing Dna Octamer, PDB code: 3iki:

Magnesium binding site 1 out of 1 in the 5-Sme-Du Containing Dna Octamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of 5-Sme-Du Containing Dna Octamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg11 b:31.3 occ:1.00 OP2 A:DG3 2.1 16.5 1.0 O A:HOH36 2.6 22.0 1.0 O A:HOH45 2.7 23.7 1.0 P A:DG3 3.4 15.7 1.0 C8 A:DG3 3.4 10.0 1.0 C3' A:UMS2 3.5 10.5 1.0 C5' A:DG3 3.5 13.7 1.0 O A:HOH32 3.7 20.0 1.0 N7 A:DG3 3.9 9.9 1.0 O3' A:UMS2 3.9 12.8 1.0 O5' A:DG3 3.9 15.2 1.0 O5' A:UMS2 4.1 8.9 1.0 C6 A:UMS2 4.1 9.1 1.0 C2' A:UMS2 4.2 10.0 1.0 O4' A:DG3 4.4 12.4 1.0 C5 A:UMS2 4.5 9.6 1.0 N1 A:UMS2 4.6 9.2 1.0 C4' A:DG3 4.6 13.2 1.0 O A:HOH26 4.6 21.2 1.0 OP2 A:UMS2 4.6 10.5 1.0 N9 A:DG3 4.6 10.2 1.0 C4' A:UMS2 4.6 9.1 1.0 OP1 A:DG3 4.7 17.1 1.0 C5' A:UMS2 4.8 8.8 1.0 C1' A:UMS2 4.9 8.9 1.0 P A:UMS2 4.9 9.1 1.0

J.Sheng, W.Zhang, A.E.Hassan, J.Gan, A.S.Soares, S.Geng, Y.Ren, Z.Huang. Hydrogen Bond Formation Between the Naturally Modified Nucleobase and Phosphate Backbone. Nucleic Acids Res. V. 40 8111 2012.
ISSN: ISSN 0305-1048
PubMed: 22641848
DOI: 10.1093/NAR/GKS426